Documentation/Nightly/Modules/AFTSegmenter - Revision history

Acsenrafilho at 13:00, 25 July 2017

2017-07-25T13:00:10Z

Acsenrafilho at 20:18, 24 July 2017

2017-07-24T20:18:59Z

Acsenrafilho at 20:09, 24 July 2017

2017-07-24T20:09:05Z

Acsenrafilho at 19:52, 24 July 2017

2017-07-24T19:52:30Z

Acsenrafilho: Created page with "{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

@@ Line 42: / Line 42: @@
 [[Image:aftsegmenter_gui.png|thumb|380px|User Interface]]
-IO:
+'''IO:'''
-*T1 Volume
+*'''T1 Volume'''
 **Input T1 volume
-*T2-FLAIR Volume
+*'''T2-FLAIR Volume'''
 **Input T2-FLAIR volume
-*Lesion Label
+*'''Lesion Label'''
 **Output a global lesion mask
-*Is brain extracted?
+*'''Is brain extracted?'''
 **Is the input data (T1 and T2-FLAIR) already brain extracted?
-Segmentation Parameters:
+'''Segmentation Parameters:'''
-*Absolute Error Threshold
+*'''Absolute Error Threshold'''
 **Define the absolute error threshold for gray matter statistics. This measure evaluated the similarity between the MNI152 template and the T2-FLAIR gray matter fluctuation estimative. A higher error gives a higher variability in the final lesion segmentation
-*Gamma
+*'''Gamma'''
 **Define the outlier detection based on units of standard deviation in the T2-FLAIR gray matter voxel intensity distribution
-*White Matter Matching
+*'''White Matter Matching'''
 **Set the local neighborhood searching for label refinement step. This metric defines the percentage of white matter tissue that surrounds the hyperintense lesions. Large values defines a conservative segmentation, i.e. in order to define a true MS lesion, it must be close to certain percentage of white matter area.
-*Minimum Lesion Size
+*'''Minimum Lesion Size'''
 **Set the minimum lesion size adopted as a true lesion in the final lesion map. Units are given in number of voxels
-*Gray Matter Mask Value
+*'''Gray Matter Mask Value'''
 **Set the mask value that represents the gray matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] module) output
-*White Matter Mask Value
+*'''White Matter Mask Value'''
 **Set the mask value that represents the white matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] module) output

@@ Line 62: / Line 62: @@
 **Set the minimum lesion size adopted as a true lesion in the final lesion map. Units are given in number of voxels
 *Gray Matter Mask Value
-**Set the mask value that represents the gray matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] extension) output
+**Set the mask value that represents the gray matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] module) output
 *White Matter Mask Value
-**Set the mask value that represents the white matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] extension) output
+**Set the mask value that represents the white matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] module) output

@@ Line 41: / Line 41: @@
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
-[[Image:lssegmenter_gui.png|thumb|380px|User Interface]]
+[[Image:aftsegmenter_gui.png|thumb|380px|User Interface]]
 IO:
 *T1 Volume

@@ Line 24: / Line 24: @@
 [[File:AFTSegmenter-icon.png|right]]
-This module offers ...
+This module offers an implementation of a recent Multiple Sclerosis lesion segmentation approach based on a unsupervised method described by Cabezas et al. <ref>Cabezas M. et al.(2014) "Automatic multiple sclerosis lesion detection in brain MRI by FLAIR thresholding", Computer Methods and Programs in Biomedicine, DOI: 10.1016/j.cmpb.2014.04.006</ref>. This module is intended to be used with FLAIR and T1 MRI volumes, which the MS lesions can be detected.
@@ Line 30: / Line 30: @@
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
 * Use Case 1: Multiple Sclerosis (MS) lesions segmentation
-**...
+**Using T1 and FLAIR MRI volumes, it can be possible to detect abnormal voxel signal using a parametric strategy, which delineates white matter signals that does not belongs to the majority neighborhood pattern. More details can be found in the original paper <ref>Cabezas M. et al.(2014) "Automatic multiple sclerosis lesion detection in brain MRI by FLAIR thresholding", Computer Methods and Programs in Biomedicine, DOI: 10.1016/j.cmpb.2014.04.006</ref>
 <gallery widths="300px" heights="300px" perrow="3">
@@ Line 44: / Line 44: @@
 IO:
 *T1 Volume
 *T2-FLAIR Volume
 *Lesion Label
 **Output a global lesion mask
+*Is brain extracted?
-Noise Attenuation Parameters:
+**Is the input data (T1 and T2-FLAIR) already brain extracted?
 Segmentation Parameters:
@@ Line 70: / Line 58: @@
 **Define the outlier detection based on units of standard deviation in the T2-FLAIR gray matter voxel intensity distribution
 *White Matter Matching
-**Set the local neighborhood searching for label refinement step. This metric defines the percentage of white matter tissue that surrounds the hyperintense lesions. Higher values defines a conservative segmentation
+**Set the local neighborhood searching for label refinement step. This metric defines the percentage of white matter tissue that surrounds the hyperintense lesions. Large values defines a conservative segmentation, i.e. in order to define a true MS lesion, it must be close to certain percentage of white matter area.
 *Minimum Lesion Size
 **Set the minimum lesion size adopted as a true lesion in the final lesion map. Units are given in number of voxels
 *Gray Matter Mask Value
-**Set the mask value that represents the gray matter. Default is defined based on the Basic Brain Tissues module output
+**Set the mask value that represents the gray matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] extension) output
 *White Matter Mask Value
-**Set the mask value that represents the white matter. Default is defined based on the Basic Brain Tissues module output
+**Set the mask value that represents the white matter. Default is defined based on the ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension Basic Brain Tissues] extension) output
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
-N/A
+*[[Documentation/Nightly/Modules/LSSegmenter|LS Segmenter]]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
-* paper
+* Cabezas, M., Oliver, A., Roura, E., Freixenet, J., Vilanova, J. C., Ramió-Torrentà, L., Rovira, À. and Lladó, X. (2014) ‘Automatic multiple sclerosis lesion detection in brain MRI by FLAIR thresholding’, Computer Methods and Programs in Biomedicine. Elsevier Ireland Ltd, 115(3), pp. 147–161. DOI: 10.1016/j.cmpb.2014.04.006.
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